conop – Connectivity and Topology of Molecules

The main task of the conop module is to interpret the topology and connectivity of proteins, polynucleotides and small molecules, e.g. after importing a structure from a PDB file. In addition, it provides an infrastructure for consistency checks.

In this module

• Functions and classes for standard amino acids
  • The AminoAcid enum
  • Converter functions
• Connectivity
  • Motivation
  • Processors
• The compound library
  • GetDefaultLib()
  • SetDefaultLib()
  • CompoundLib
  • Compound
  • AtomSpec
  • BondSpec
  • Example: Translating SEQRES entries
  • Creating a compound library
• conop.cleanup – Sanitize structures
  • Cleanup()
• Conop Functions
  • AssignBackboneTorsions()
  • IsBondFeasible()
  • GetUnknownAtomsOfResidue()